DNA barcoding is a promising taxon identification tool based on the analysis of a standardized DNA fragment,relying on the assumption that genetic variation between species exceeds that within species. This method can be essential for identifying samples when morphological characters are lacking or insufficient and it can be applied in several fields, encompassing biodiversity surveys, species discovery, forensics, biocontrol, studies of historical distribution pattern and plant-animal interactions. Nonetheless, the applicability of DNA barcoding for plant species identification is often limited by the absence of a unique, universal and efficient DNA barcode, and particularly for land plant, by the lack of sequences for many taxa in public reference databases The present study is thus focused on the comparison of three plastidial DNA markers, i.e. rbcLa, matK and trnH-psbA, and one nuclear ribosomal marker, i.e. ITS2, for the identification of 25 threatened and protected alpine land plant speciesfrom 14 different families. The efficiency of each barcode was assessed in terms of amplification and sequencing success, as well as the ability to correctly identify the related species.Starting from 123 foliar samples, either freshly collected or from herbarium specimens, rbcLa showed a 100% amplification and sequencing success, whereas trnH-psbA, matK and ITS2, displayed lower success rates of 90%, 87% and 85% respectively. These lower rates were mainly due to problems linked to the universality of primers or the quality of DNA extracts from old herbarium specimens or the presence of homopolymers and INDELs in the barcode sequence. Conversely, the ability of detecting a barcoding gap, allowing a correct species identification, was higher for trnH-psbA, ITS2 and matK, 68%, 58% and 54% respectively, compared to rbcLa at 32%. However, combining all four barcodes, all species were correctly identified, except one, Potentilla pensylvanica, which was identified as Potentilla hispanica. This finding will require further investigation. Overall, this study added 445 sequences of land plant species to public reference database and confirmed the need to use multiple barcodes to support identifications in floristic inventories.
DNA barcoding of alpine flora in Aosta Valley
Comino C.;Portis E
2025-01-01
Abstract
DNA barcoding is a promising taxon identification tool based on the analysis of a standardized DNA fragment,relying on the assumption that genetic variation between species exceeds that within species. This method can be essential for identifying samples when morphological characters are lacking or insufficient and it can be applied in several fields, encompassing biodiversity surveys, species discovery, forensics, biocontrol, studies of historical distribution pattern and plant-animal interactions. Nonetheless, the applicability of DNA barcoding for plant species identification is often limited by the absence of a unique, universal and efficient DNA barcode, and particularly for land plant, by the lack of sequences for many taxa in public reference databases The present study is thus focused on the comparison of three plastidial DNA markers, i.e. rbcLa, matK and trnH-psbA, and one nuclear ribosomal marker, i.e. ITS2, for the identification of 25 threatened and protected alpine land plant speciesfrom 14 different families. The efficiency of each barcode was assessed in terms of amplification and sequencing success, as well as the ability to correctly identify the related species.Starting from 123 foliar samples, either freshly collected or from herbarium specimens, rbcLa showed a 100% amplification and sequencing success, whereas trnH-psbA, matK and ITS2, displayed lower success rates of 90%, 87% and 85% respectively. These lower rates were mainly due to problems linked to the universality of primers or the quality of DNA extracts from old herbarium specimens or the presence of homopolymers and INDELs in the barcode sequence. Conversely, the ability of detecting a barcoding gap, allowing a correct species identification, was higher for trnH-psbA, ITS2 and matK, 68%, 58% and 54% respectively, compared to rbcLa at 32%. However, combining all four barcodes, all species were correctly identified, except one, Potentilla pensylvanica, which was identified as Potentilla hispanica. This finding will require further investigation. Overall, this study added 445 sequences of land plant species to public reference database and confirmed the need to use multiple barcodes to support identifications in floristic inventories.
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